Dataset Information

Cell segmentation and tracking using CNN-based distance predictions and a graph-based matching strategy.

ABSTRACT: The accurate segmentation and tracking of cells in microscopy image sequences is an important task in biomedical research, e.g., for studying the development of tissues, organs or entire organisms. However, the segmentation of touching cells in images with a low signal-to-noise-ratio is still a challenging problem. In this paper, we present a method for the segmentation of touching cells in microscopy images. By using a novel representation of cell borders, inspired by distance maps, our method is capable to utilize not only touching cells but also close cells in the training process. Furthermore, this representation is notably robust to annotation errors and shows promising results for the segmentation of microscopy images containing in the training data underrepresented or not included cell types. For the prediction of the proposed neighbor distances, an adapted U-Net convolutional neural network (CNN) with two decoder paths is used. In addition, we adapt a graph-based cell tracking algorithm to evaluate our proposed method on the task of cell tracking. The adapted tracking algorithm includes a movement estimation in the cost function to re-link tracks with missing segmentation masks over a short sequence of frames. Our combined tracking by detection method has proven its potential in the IEEE ISBI 2020 Cell Tracking Challenge (http://celltrackingchallenge.net/) where we achieved as team KIT-Sch-GE multiple top three rankings including two top performances using a single segmentation model for the diverse data sets.

SUBMITTER: Scherr T

PROVIDER: S-EPMC7723299 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Cell segmentation and tracking using CNN-based distance predictions and a graph-based matching strategy.

Scherr Tim T Löffler Katharina K Böhland Moritz M Mikut Ralf R

PloS one 20201208 12

The accurate segmentation and tracking of cells in microscopy image sequences is an important task in biomedical research, e.g., for studying the development of tissues, organs or entire organisms. However, the segmentation of touching cells in images with a low signal-to-noise-ratio is still a challenging problem. In this paper, we present a method for the segmentation of touching cells in microscopy images. By using a novel representation of cell borders, inspired by distance maps, our method ...[more]

PMID: 33290432

Similar Datasets

Project description:PURPOSE:Cardiac image segmentation is a critical process for generating personalized models of the heart and for quantifying cardiac performance parameters. Fully automatic segmentation of the left ventricle (LV), the right ventricle (RV), and the myocardium from cardiac cine MR images is challenging due to variability of the normal and abnormal anatomy, as well as the imaging protocols. This study proposes a multi-task learning (MTL)-based regularization of a convolutional neural network (CNN) to obtain accurate segmenation of the cardiac structures from cine MR images. METHODS:We train a CNN network to perform the main task of semantic segmentation, along with the simultaneous, auxiliary task of pixel-wise distance map regression. The network also predicts uncertainties associated with both tasks, such that their losses are weighted by the inverse of their corresponding uncertainties. As a result, during training, the task featuring a higher uncertainty is weighted less and vice versa. The proposed distance map regularizer is a decoder network added to the bottleneck layer of an existing CNN architecture, facilitating the network to learn robust global features. The regularizer block is removed after training, so that the original number of network parameters does not change. The trained network outputs per-pixel segmentation when a new patient cine MR image is provided as an input. RESULTS:We show that the proposed regularization method improves both binary and multi-class segmentation performance over the corresponding state-of-the-art CNN architectures. The evaluation was conducted on two publicly available cardiac cine MRI datasets, yielding average Dice coefficients of 0.84 ± 0.03 and 0.91 ± 0.04. We also demonstrate improved generalization performance of the distance map regularized network on cross-dataset segmentation, showing as much as 42% improvement in myocardium Dice coefficient from 0.56 ± 0.28 to 0.80 ± 0.14. CONCLUSIONS:We have presented a method for accurate segmentation of cardiac structures from cine MR images. Our experiments verify that the proposed method exceeds the segmentation performance of three existing state-of-the-art methods. Furthermore, several cardiac indices that often serve as diagnostic biomarkers, specifically blood pool volume, myocardial mass, and ejection fraction, computed using our method are better correlated with the indices computed from the reference, ground truth segmentation. Hence, the proposed method has the potential to become a non-invasive screening and diagnostic tool for the clinical assessment of various cardiac conditions, as well as a reliable aid for generating patient specific models of the cardiac anatomy for therapy planning, simulation, and guidance.

Project description:Purpose: More and more automatic segmentation tools are being introduced in routine clinical practice. However, physicians need to spend a considerable amount of time in examining the generated contours slice by slice. This greatly reduces the benefit of the tool's automaticity. In order to overcome this shortcoming, we developed an automatic quality assurance (QA) method for automatic segmentation using convolutional neural networks (CNNs). Materials and Methods: The study cohort comprised 680 patients with early-stage breast cancer who received whole breast radiation. The overall architecture of the automatic QA method for deep learning-based segmentation included the following two main parts: a segmentation CNN model and a QA network that was established based on ResNet-101. The inputs were from computed tomography, segmentation probability maps, and uncertainty maps. Two kinds of Dice similarity coefficient (DSC) outputs were tested. One predicted the DSC quality level of each slice ([0.95, 1] for "good," [0.8, 0.95] for "medium," and [0, 0.8] for "bad" quality), and the other predicted the DSC value of each slice directly. The performances of the method to predict the quality levels were evaluated with quantitative metrics: balanced accuracy, F score, and the area under the receiving operator characteristic curve (AUC). The mean absolute error (MAE) was used to evaluate the DSC value outputs. Results: The proposed methods involved two types of output, both of which achieved promising accuracy in terms of predicting the quality level. For the good, medium, and bad quality level prediction, the balanced accuracy was 0.97, 0.94, and 0.89, respectively; the F score was 0.98, 0.91, and 0.81, respectively; and the AUC was 0.96, 0.93, and 0.88, respectively. For the DSC value prediction, the MAE was 0.06 ± 0.19. The prediction time was approximately 2 s per patient. Conclusions: Our method could predict the segmentation quality automatically. It can provide useful information for physicians regarding further verification and revision of automatic contours. The integration of our method into current automatic segmentation pipelines can improve the efficiency of radiotherapy contouring.

Dataset Information

Cell segmentation and tracking using CNN-based distance predictions and a graph-based matching strategy.

Publications

Cell segmentation and tracking using CNN-based distance predictions and a graph-based matching strategy.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets